I think optimizing theme images would be possible. However, due to copyrights and other notices that could be stripped by this plugin, I think it would not be wise to do so. You can certainly optimize any images in your theme with the commands found on the FAQ, or any GUIs that may be available for the tools used by this plugin.
Regarding your request for custom directories, it would be a security risk to process arbitrary directories outside of the wordpress media library by way of this plugin. This would allow a wordpress admin to modify images in directories where they may not be otherwise permitted to have access (potentially anywhere that the webserver has ‘write’ access). Again, you could use the commands in the FAQ to serve this purpose, and there are ways of creating scripts to process whole directories (with sub-directories).
